Computer & Information Sciences

PLOS Computational Biology: Software

Published April 20, 2020 Curated Collections

The PLOS Computational Biology Software Section was launched in 2011 and has been steadily gathering momentum since its beginnings. Handled by our Software Editors, Software articles highlight and describe outstanding open source software of exceptional importance that has been shown to provide new biological insights, either as a part of the Software article, or published elsewhere.

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Editorials

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PLOS Computational Biology The PLOS Computational Biology Software Section
November 29, 2012 Andreas Prlić, Hilmar Lapp
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PLOS

PLOS Computational Biology Ten Simple Rules for the Open Development of Scientific Software
December 6, 2012 Andreas Prlić, James B. Procter

Blog

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Biologue Software Collection: Open Access meets Open Source in PLOS Computational Biology
November 30, 2012 Chris Hall
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PLOS Blogs PLOS Computational Biology Software Collection: The Combination of Open Access and Open Source Accelerates Scientific Research – The Official PLOS Blog
November 29, 2012 Victoria Costello

Research

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10.1371/journal.pcbi.1007781

PLOS Computational Biology PlasClass improves plasmid sequence classification
April 3, 2020 David Pellow, Itzik Mizrahi, Ron Shamir
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10.1371/journal.pcbi.1007747

PLOS Computational Biology ProteinVR: Web-based molecular visualization in virtual reality
March 31, 2020 Kevin C. Cassidy, Jan Šefčík, Yogindra Raghav, Alexander Chang, Jacob D. Durrant
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10.1371/journal.pcbi.1007665

PLOS Computational Biology CAncer bioMarker Prediction Pipeline (CAMPP)—A standardized framework for the analysis of quantitative biological data
March 16, 2020 Thilde Terkelsen, Anders Krogh, Elena Papaleo
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10.1371/journal.pcbi.1007654

PLOS Computational Biology ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data
March 16, 2020 Lisa M. Bramer, Amanda M. White, Kelly G. Stratton, Allison M. Thompson, Daniel Claborne, Kirsten Hofmockel, Lee Ann McCue
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10.1371/journal.pcbi.1007635

PLOS Computational Biology Hybrid Automata Library: A flexible platform for hybrid modeling with real-time visualization
March 10, 2020 Rafael R. Bravo, Etienne Baratchart, Jeffrey West, Ryan O. Schenck, Anna K. Miller, Jill Gallaher, Chandler D. Gatenbee, David Basanta, Mark Robertson-Tessi, Alexander R. A. Anderson
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10.1371/journal.pcbi.1007741

PLOS Computational Biology ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis
March 9, 2020 Arshag D. Mooradian, Sjoerd van der Post, Kristen M. Naegle, Jason M. Held
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10.1371/journal.pcbi.1007134

PLOS Computational Biology ASA³P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates
March 5, 2020 Oliver Schwengers, Andreas Hoek, Moritz Fritzenwanker, Linda Falgenhauer, Torsten Hain, Trinad Chakraborty, Alexander Goesmann
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10.1371/journal.pcbi.1007664

PLOS Computational Biology Tximeta: Reference sequence checksums for provenance identification in RNA-seq
February 25, 2020 Michael I. Love, Charlotte Soneson, Peter F. Hickey, Lisa K. Johnson, N. Tessa Pierce, Lori Shepherd, Martin Morgan, Rob Patro
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10.1371/journal.pcbi.1007696

PLOS Computational Biology The SONATA data format for efficient description of large-scale network models
February 24, 2020 Kael Dai, Juan Hernando, Yazan N. Billeh, Sergey L. Gratiy, Judit Planas, Andrew P. Davison, Salvador Dura-Bernal, Padraig Gleeson, Adrien Devresse, Benjamin K. Dichter, Michael Gevaert, James G. King, Werner A. H. Van Geit, Arseny V. Povolotsky, Eilif Muller, Jean-Denis Courcol, Anton Arkhipov
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10.1371/journal.pcbi.1007663

PLOS Computational Biology RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method
February 14, 2020 Kosuke Hamazaki, Hiroyoshi Iwata
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10.1371/journal.pcbi.1007503

PLOS Computational Biology CovCopCan: An efficient tool to detect Copy Number Variation from amplicon sequencing data in inherited diseases and cancer
February 12, 2020 Paco Derouault, Jasmine Chauzeix, David Rizzo, Federica Miressi, Corinne Magdelaine, Sylvie Bourthoumieu, Karine Durand, Hélène Dzugan, Jean Feuillard, Franck Sturtz, Stéphane Mérillou, Anne-Sophie Lia
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10.1371/journal.pcbi.1007613

PLOS Computational Biology SmartPhase: Accurate and fast phasing of heterozygous variant pairs for genetic diagnosis of rare diseases
February 7, 2020 Paul Hager, Hans-Werner Mewes, Meino Rohlfs, Christoph Klein, Tim Jeske
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10.1371/journal.pcbi.1007313

PLOS Computational Biology Orbit Image Analysis: An open-source whole slide image analysis tool
February 5, 2020 Manuel Stritt, Anna K. Stalder, Enrico Vezzali
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10.1371/journal.pcbi.1007604

PLOS Computational Biology SynToxProfiler: An interactive analysis of drug combination synergy, toxicity and efficacy
February 3, 2020 Aleksandr Ianevski, Sanna Timonen, Alexander Kononov, Tero Aittokallio, Anil K. Giri
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10.1371/journal.pcbi.1007625

PLOS Computational Biology XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data
January 31, 2020 Jordan A. Berg, Jonathan R. Belyeu, Jeffrey T. Morgan, Yeyun Ouyang, Alex J. Bott, Aaron R. Quinlan, Jason Gertz, Jared Rutter
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10.1371/journal.pcbi.1007549

PLOS Computational Biology BrainIAK tutorials: User-friendly learning materials for advanced fMRI analysis
January 15, 2020 Manoj Kumar, Cameron T. Ellis, Qihong Lu, Hejia Zhang, Mihai Capotă, Theodore L. Willke, Peter J. Ramadge, Nicholas B. Turk-Browne, Kenneth A. Norman
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10.1371/journal.pcbi.1007598

PLOS Computational Biology DetEdit: A graphical user interface for annotating and editing events detected in long-term acoustic monitoring data
January 13, 2020 Alba Solsona-Berga, Kaitlin Frasier, Simone Baumann-Pickering, Sean Wiggins, John Hildebrand
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10.1371/journal.pcbi.1007556

PLOS Computational Biology ForestQC: Quality control on genetic variants from next-generation sequencing data using random forest
December 18, 2019 Jiajin Li, Brandon Jew, Lingyu Zhan, Sungoo Hwang, Giovanni Coppola, Nelson B. Freimer, Jae Hoon Sul
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10.1371/journal.pcbi.1007125

PLOS Computational Biology NUFEB: A massively parallel simulator for individual-based modelling of microbial communities
December 12, 2019 Bowen Li, Denis Taniguchi, Jayathilake Pahala Gedara, Valentina Gogulancea, Rebeca Gonzalez-Cabaleiro, Jinju Chen, Andrew Stephen McGough, Irina Dana Ofiteru, Thomas P. Curtis, Paolo Zuliani
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10.1371/journal.pcbi.1007453

PLOS Computational Biology TAPES: A tool for assessment and prioritisation in exome studies
October 15, 2019 Alexandre Xavier, Rodney J. Scott, Bente A. Talseth-Palmer
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10.1371/journal.pcbi.1007342

PLOS Computational Biology EMULSION: Transparent and flexible multiscale stochastic models in human, animal and plant epidemiology
September 13, 2019 Sébastien Picault, Yu-Lin Huang, Vianney Sicard, Sandie Arnoux, Gaël Beaunée, Pauline Ezanno
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10.1371/journal.pcbi.1006940

PLOS Computational Biology CNEr: A toolkit for exploring extreme noncoding conservation
August 26, 2019 Ge Tan, Dimitris Polychronopoulos, Boris Lenhard
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10.1371/journal.pcbi.1007227

PLOS Computational Biology PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks
August 19, 2019 Jianan Lin, Yuping Zhang, Wayne N. Frankel, Zhengqing Ouyang
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10.1371/journal.pcbi.1007082

PLOS Computational Biology DART-ID increases single-cell proteome coverage
July 1, 2019 Albert Tian Chen, Alexander Franks, Nikolai Slavov
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10.1371/journal.pcbi.1007128

PLOS Computational Biology Open collaborative writing with Manubot
June 24, 2019 Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
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10.1371/journal.pcbi.1006971

PLOS Computational Biology BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data
April 22, 2019 Jean-Christophe Lachance, Colton J. Lloyd, Jonathan M. Monk, Laurence Yang, Anand V. Sastry, Yara Seif, Bernhard O. Palsson, Sébastien Rodrigue, Adam M. Feist, Zachary A. King, Pierre-Étienne Jacques
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10.1371/journal.pcbi.1006650

PLOS Computational Biology BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
April 8, 2019 Remco Bouckaert, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, David Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, Alexei J. Drummond
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10.1371/journal.pcbi.1006967

PLOS Computational Biology Recentrifuge: Robust comparative analysis and contamination removal for metagenomics
April 8, 2019 Jose Manuel Martí
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10.1371/journal.pcbi.1006699

PLOS Computational Biology Stytra: An open-source, integrated system for stimulation, tracking and closed-loop behavioral experiments
April 8, 2019 Vilim Štih, Luigi Petrucco, Andreas M. Kist, Ruben Portugues
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10.1371/journal.pcbi.1006899

PLOS Computational Biology Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE)
April 2, 2019 Hailong Meng, Gur Yaari, Christopher R. Bolen, Stefan Avey, Steven H. Kleinstein
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10.1371/journal.pcbi.1006847

PLOS Computational Biology Searching algorithm for Type IV effector proteins (S4TE) 2.0: Improved tools for Type IV effector prediction, analysis and comparison in proteobacteria
March 25, 2019 Christophe Noroy, Thierry Lefrançois, Damien F. Meyer
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10.1371/journal.pcbi.1006701

PLOS Computational Biology New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx
March 5, 2019 Mohamed Mounir, Marta Lucchetta, Tiago C. Silva, Catharina Olsen, Gianluca Bontempi, Xi Chen, Houtan Noushmehr, Antonio Colaprico, Elena Papaleo
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10.1371/journal.pcbi.1006830

PLOS Computational Biology ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics
February 28, 2019 Moritz Hoffmann, Christoph Fröhner, Frank Noé
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10.1371/journal.pcbi.1006843

PLOS Computational Biology Script of Scripts: A pragmatic workflow system for daily computational research
February 27, 2019 Gao Wang, Bo Peng
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10.1371/journal.pcbi.1006792

PLOS Computational Biology IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis
February 14, 2019 Brandon Monier, Adam McDermaid, Cankun Wang, Jing Zhao, Allison Miller, Anne Fennell, Qin Ma
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10.1371/journal.pcbi.1006791

PLOS Computational Biology BioJava 5: A community driven open-source bioinformatics library
February 8, 2019 Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, Jose M. Duarte
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10.1371/journal.pcbi.1006790

PLOS Computational Biology Apollo: Democratizing genome annotation
February 6, 2019 Nathan A. Dunn, Deepak R. Unni, Colin Diesh, Monica Munoz-Torres, Nomi L. Harris, Eric Yao, Helena Rasche, Ian H. Holmes, Christine G. Elsik, Suzanna E. Lewis
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10.1371/journal.pcbi.1006718

PLOS Computational Biology DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network
February 4, 2019 Limeng Pu, Rajiv Gandhi Govindaraj, Jeffrey Mitchell Lemoine, Hsiao-Chun Wu, Michal Brylinski
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10.1371/journal.pcbi.1006384

PLOS Computational Biology Context-explorer: Analysis of spatially organized protein expression in high-throughput screens
January 2, 2019 Joel Ostblom, Emanuel J. P. Nazareth, Mukul Tewary, Peter W. Zandstra
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10.1371/journal.pcbi.1006498

PLOS Computational Biology Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons
December 13, 2018 Kemal Eren, Steven Weaver, Robert Ketteringham, Morné Valentyn, Melissa Laird Smith, Venkatesh Kumar, Sanjay Mohan, Sergei L. Kosakovsky Pond, Ben Murrell
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Tronnolone et al.

PLOS Computational Biology TAMMiCol: Tool for analysis of the morphology of microbial colonies
December 3, 2018 Hayden Tronnolone, Jennifer M. Gardner, Joanna F. Sundstrom, Vladimir Jiranek, Stephen G. Oliver, Benjamin J. Binder
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Wick et al.

PLOS Computational Biology Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks
November 20, 2018 Ryan Wick, Louise Judd, Kathryn Holt
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10.1371/journal.pcbi.1006546

PLOS Computational Biology Bayesian phylodynamic inference with complex models
November 13, 2018 Erik M. Volz, Igor Siveroni
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10.1371/journal.pcbi.1006378

PLOS Computational Biology clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets
September 4, 2018 Davide Risso, Liam Purvis, Russell B. Fletcher, Diya Das, John Ngai, Sandrine Dudoit, Elizabeth Purdom
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10.1371/journal.pcbi.1006387

PLOS Computational Biology NFTsim: Theory and Simulation of Multiscale Neural Field Dynamics
August 22, 2018 Paula Sanz-Leon, Peter A. Robinson, Stuart A. Knock, Peter M. Drysdale, Romesh G. Abeysuriya, Felix K. Fung, Chris J. Rennie, Xuelong Zhao
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10.1371/journal.pcbi.1006360

PLOS Computational Biology ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization
August 17, 2018 Diego Garrido-Martín, Emilio Palumbo, Roderic Guigó, Alessandra Breschi
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10.1371/journal.pcbi.1006413

PLOS Computational Biology MimicrEE2: Genome-wide forward simulations of Evolve and Resequencing studies
August 16, 2018 Christos Vlachos, Robert Kofler
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10.1371/journal.pcbi.1006369

PLOS Computational Biology SILGGM: An extensive R package for efficient statistical inference in large-scale gene networks
August 13, 2018 Rong Zhang, Zhao Ren, Wei Chen
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10.1371/journal.pcbi.1006169

PLOS Computational Biology riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data
August 13, 2018 Fabio Lauria, Toma Tebaldi, Paola Bernabò, Ewout J. N. Groen, Thomas H. Gillingwater, Gabriella Viero
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10.1371/journal.pcbi.1006361

PLOS Computational Biology scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data
August 10, 2018 Luyi Tian, Shian Su, Xueyi Dong, Daniela Amann-Zalcenstein, Christine Biben, Azadeh Seidi, Douglas J. Hilton, Shalin H. Naik, Matthew E. Ritchie
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10.1371/journal.pcbi.1006223

PLOS Computational Biology OpenSim: Simulating musculoskeletal dynamics and neuromuscular control to study human and animal movement
July 26, 2018 Ajay Seth, Jennifer L. Hicks, Thomas K. Uchida, Ayman Habib, Christopher L. Dembia, James J. Dunne, Carmichael F. Ong, Matthew S. DeMers, Apoorva Rajagopal, Matthew Millard, Samuel R. Hamner, Edith M. Arnold, Jennifer R. Yong, Shrinidhi K. Lakshmikanth, Michael A. Sherman, Joy P. Ku, Scott L. Delp
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10.1371/journal.pcbi.1006343

PLOS Computational Biology PyPhi: A toolbox for integrated information theory
July 26, 2018 William G. P. Mayner, William Marshall, Larissa Albantakis, Graham Findlay, Robert Marchman, Giulio Tononi
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10.1371/journal.pcbi.1006302

PLOS Computational Biology COBRAme: A computational framework for genome-scale models of metabolism and gene expression
July 5, 2018 Colton J. Lloyd, Ali Ebrahim, Laurence Yang, Zachary A. King, Edward Catoiu, Edward J. O’Brien, Joanne K. Liu, Bernhard O. Palsson
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Zappia et al.

PLOS Computational Biology Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database
June 25, 2018 Luke Zappia, Belinda Phipson, Alicia Oshlack
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Medley et al.

PLOS Computational Biology Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology
June 15, 2018 J. Kyle Medley, Kiri Choi, Matthias König, Lucian Smith, Stanley Gu, Joseph Hellerstein, Stuart C. Sealfon, Herbert M. Sauro
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Henry et al.

PLOS Computational Biology φ-evo: A program to evolve phenotypic models of biological networks
June 11, 2018 Adrien Henry, Mathieu Hemery, Paul François
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10.1371/journal.pcbi.1006064

PLOS Computational Biology Porcupine: A visual pipeline tool for neuroimaging analysis
May 10, 2018 Tim van Mourik, Lukas Snoek, Tomas Knapen, David G. Norris
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Lun et al.

PLOS Computational Biology beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types
May 3, 2018 Aaron T. L. Lun, Hervé Pagès, Mike L. Smith
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10.1371/journal.pcbi.1006090

PLOS Computational Biology DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP
April 23, 2018 Sneha Mitra, Anushua Biswas, Leelavati Narlikar
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10.1371/journal.pcbi.1006128

PLOS Computational Biology EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos
April 19, 2018 Benjamin Schott, Manuel Traub, Cornelia Schlagenhauf, Masanari Takamiya, Thomas Antritter, Andreas Bartschat, Katharina Löffler, Denis Blessing, Jens C. Otte, Andrei Y. Kobitski, G. Ulrich Nienhaus, Uwe Strähle, Ralf Mikut, Johannes Stegmaier
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10.1371/journal.pcbi.1006079

PLOS Computational Biology Biobeam—Multiplexed wave-optical simulations of light-sheet microscopy
April 13, 2018 Martin Weigert, Kaushikaram Subramanian, Sebastian T. Bundschuh, Eugene W. Myers, Moritz Kreysing
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Prada et al.

PLOS Computational Biology An open source tool for automatic spatiotemporal assessment of calcium transients and local ‘signal-close-to-noise’ activity in calcium imaging data
March 30, 2018 Juan Prada, Manju Sasi, Corinna Martin, Sibylle Jablonka, Thomas Dandekar, Robert Blum
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Solernou et al.

PLOS Computational Biology Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules
March 23, 2018 Albert Solernou, Benjamin S. Hanson, Robin A. Richardson, Robert Welch, Daniel J. Read, Oliver G. Harlen, Sarah A. Harris
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10.1371/journal.pcbi.1006019

PLOS Computational Biology iDREM: Interactive visualization of dynamic regulatory networks
March 14, 2018 Jun Ding, James S. Hagood, Namasivayam Ambalavanan, Naftali Kaminski, Ziv Bar-Joseph
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10.1371/journal.pcbi.1006058

PLOS Computational Biology LAILAPS-QSM: A RESTful API and JAVA library for semantic query suggestions
March 12, 2018 Jinbo Chen, Uwe Scholz, Ruonan Zhou, Matthias Lange
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10.1371/journal.pcbi.1006018

PLOS Computational Biology speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification
March 1, 2018 Charlie Beirnaert, Pieter Meysman, Trung Nghia Vu, Nina Hermans, Sandra Apers, Luc Pieters, Adrian Covaci, Kris Laukens
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10.1371/journal.pcbi.1005968

PLOS Computational Biology Reactome graph database: Efficient access to complex pathway data
January 29, 2018 Antonio Fabregat, Florian Korninger, Guilherme Viteri, Konstantinos Sidiropoulos, Pablo Marin-Garcia, Peipei Ping, Guanming Wu, Lincoln Stein, Peter D’Eustachio, Henning Hermjakob
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10.1371/journal.pcbi.1005944

PLOS Computational Biology MUMmer4: A fast and versatile genome alignment system
January 26, 2018 Guillaume Marçais, Arthur L. Delcher, Adam M. Phillippy, Rachel Coston, Steven L. Salzberg, Aleksey Zimin
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10.1371/journal.pcbi.1005950

PLOS Computational Biology HaSAPPy: A tool for candidate identification in pooled forward genetic screens of haploid mammalian cells
January 16, 2018 Giulio Di Minin, Andreas Postlmayr, Anton Wutz
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10.1371/journal.pcbi.1005900

PLOS Computational Biology Bowhead: Bayesian modelling of cell velocity during concerted cell migration
January 8, 2018 Mathias Engel, James Longden, Jesper Ferkinghoff-Borg, Xavier Robin, Gaye Saginc, Rune Linding
PLOS Computational Biology MAGPIE: Simplifying access and execution of computational models in the life sciences
December 15, 2017 Christoph Baldow, Sebastian Salentin, Michael Schroeder, Ingo Roeder, Ingmar Glauche
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10.1371/journal.pcbi.1005867

PLOS Computational Biology Predicting the pathogenicity of novel variants in mitochondrial tRNA with MitoTIP
December 11, 2017 Sanjay Sonney, Jeremy Leipzig, Marie T. Lott, Shiping Zhang, Vincent Procaccio, Douglas C. Wallace, Neal Sondheimer
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10.1371/journal.pcbi.1005865

PLOS Computational Biology pSSAlib: The partial-propensity stochastic chemical network simulator
December 4, 2017 Oleksandr Ostrenko, Pietro Incardona, Rajesh Ramaswamy, Lutz Brusch, Ivo F. Sbalzarini
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10.1371/journal.pcbi.1005838

PLOS Computational Biology fluEvidenceSynthesis: An R package for evidence synthesis based analysis of epidemiological outbreaks
November 20, 2017 Edwin van Leeuwen, Petra Klepac, Dominic Thorrington, Richard Pebody, Marc Baguelin
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10.1371/journal.pcbi.1005752

PLOS Computational Biology mixOmics: An R package for ‘omics feature selection and multiple data integration
November 3, 2017 Florian Rohart, Benoît Gautier, Amrit Singh, Kim-Anh Lê Cao
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10.1371/journal.pcbi.1005598

PLOS Computational Biology Network propagation in the cytoscape cyberinfrastructure
October 12, 2017 Daniel Carlin, Barry Demchak, Dexter Pratt, Eric Sage, Trey Ideker
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10.1371/journal.pcbi.1005727

PLOS Computational Biology kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
September 5, 2017 Kevin D. Murray, Christfried Webers, Cheng Soon Ong, Justin Borevitz, Norman Warthmann
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PLOS

PLOS Computational Biology PCSF: An R-package for network-based interpretation of high-throughput data
July 31, 2017 Murodzhon Akhmedov, Amanda Kedaigle, Renan Escalante Chong, Roberto Montemanni, Francesco Bertoni, Ernest Fraenkel, Ivo Kwee
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10.1371/journal.pcbi.1005659

PLOS Computational Biology OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
July 26, 2017 Peter Eastman, Jason Swails, John D. Chodera, Robert T. McGibbon, Yutong Zhao, Kyle A. Beauchamp, Lee-Ping Wang, Andrew C. Simmonett, Matthew P. Harrigan, Chaya D. Stern, Rafal P. Wiewiora, Bernard R. Brooks, Vijay S. Pande
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10.1371/journal.pcbi.1005665

PLOS Computational Biology Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors
July 19, 2017 François Serra, Davide Baù, Mike Goodstadt, David Castillo, Guillaume J. Filion, Marc A. Marti-Renom
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10.1371/journal.pcbi.1005520

PLOS Computational Biology Mendel,MD: A user-friendly open-source web tool for analyzing WES and WGS in the diagnosis of patients with Mendelian disorders
June 8, 2017 Raony G. C. C. L. Cardenas, Natália D. Linhares, Raquel L. Ferreira, Sérgio D. J. Pena
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10.1371/journal.pcbi.1005595

PLOS Computational Biology Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
June 8, 2017 Ryan R. Wick, Louise M. Judd, Claire L. Gorrie, Kathryn E. Holt
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10.1371/journal.pcbi.1005526

PLOS Computational Biology An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics
June 7, 2017 Sebastián A. Romano, Verónica Pérez-Schuster, Adrien Jouary, Jonathan Boulanger-Weill, Alessia Candeo, Thomas Pietri, Germán Sumbre
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10.1371/journal.pcbi.1005575

PLOS Computational Biology MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures
June 2, 2017 Anthony R. Bradley, Alexander S. Rose, Antonín Pavelka, Yana Valasatava, Jose M. Duarte, Andreas Prlić, Peter W. Rose
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10.1371/journal.pcbi.1005430

PLOS Computational Biology Hard real-time closed-loop electrophysiology with the Real-Time eXperiment Interface (RTXI)
May 30, 2017 Yogi A. Patel, Ansel George, Alan D. Dorval, John A. White, David J. Christini, Robert J. Butera
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10.1371/journal.pcbi.1005564

PLOS Computational Biology sourceR: Classification and source attribution of infectious agents among heterogeneous populations
May 30, 2017 Poppy Miller, Jonathan Marshall, Nigel French, Chris Jewell
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10.1371/journal.pcbi.1005562

PLOS Computational Biology ROTS: An R package for reproducibility-optimized statistical testing
May 25, 2017 Tomi Suomi, Fatemeh Seyednasrollah, Maria K. Jaakkola, Thomas Faux, Laura L. Elo
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10.1371/journal.pcbi.1005528

PLOS Computational Biology PyLDM – An open source package for lifetime density analysis of time-resolved spectroscopic data
May 22, 2017 Gabriel F. Dorlhiac, Clyde Fare, Jasper J. van Thor
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10.1371/journal.pcbi.1005530

PLOS Computational Biology FIMTrack: An open source tracking and locomotion analysis software for small animals
May 11, 2017 Benjamin Risse, Dimitri Berh, Nils Otto, Christian Klämbt, Xiaoyi Jiang
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10.1371/journal.pcbi.1005480

PLOS Computational Biology MAGERI: computational pipeline for molecular-barcoded targeted resequencing
May 5, 2017 Mikhail Shugay, Andrew Zaretsky, Dmitriy Shagin, Irina Shagina, Ivan Volchenkov, Andrew Shelenkov, Mikhail Lebedin, Dmitriy Bagaev, Sergey Lukyanov, Dmitriy Chudakov
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10.1371/journal.pcbi.1005518

PLOS Computational Biology ESPRIT-Forest: Parallel clustering of massive amplicon sequence data in subquadratic time
April 24, 2017 Yunpeng Cai, Wei Zheng, Jin Yao, Yujie Yang, Volker Mai, Qi Mao, Yijun Sun
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10.1371/journal.pcbi.1005467

PLOS Computational Biology ARACHNE: A neural-neuroglial network builder with remotely controlled parallel computing
March 31, 2017 Sergey G. Aleksin, Kaiyu Zheng, Dmitri A. Rusakov, Leonid P. Savtchenko
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10.1371/journal.pcbi.1005209

PLOS Computational Biology BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods
March 9, 2017 Krzysztof J. Gorgolewski, Fidel Alfaro-Almagro, Tibor Auer, Pierre Bellec, Mihai Capotă, M. Mallar Chakravarty, Nathan W. Churchill, Alexander Li Cohen, R. Cameron Craddock, Gabriel A. Devenyi, Anders Eklund, Oscar Esteban, Guillaume Flandin, Satrajit S. Ghosh, J. Swaroop Guntupalli, Mark Jenkinson, Anisha Keshavan, Gregory Kiar, Franziskus Liem, Pradeep Reddy Raamana, David Raffelt, Christopher J. Steele, Pierre-Olivier Quirion, Robert E. Smith, Stephen C. Strother, Gaël Varoquaux, Yida Wang, Tal Yarkoni, Russell A. Poldrack
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10.1371/journal.pcbi.1005350

PLOS Computational Biology Mindboggling morphometry of human brains
February 23, 2017 Arno Klein, Satrajit S. Ghosh, Forrest S. Bao, Joachim Giard, Yrjö Häme, Eliezer Stavsky, Noah Lee, Brian Rossa, Martin Reuter, Elias Chaibub Neto, Anisha Keshavan
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10.1371/journal.pcbi.1005404

PLOS Computational Biology Metacoder: An R package for visualization and manipulation of community taxonomic diversity data
February 21, 2017 Zachary S. L. Foster, Thomas J. Sharpton, Niklaus J. Grünwald
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10.1371/journal.pcbi.1005351

PLOS Computational Biology ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour
February 3, 2017 Stephanie Evans, Lourdes Cucurull-Sanchez, Christopher Larminie, Mark C. Coles, Marika C. Kullberg, Jon Timmis, Kieran Alden
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10.1371/journal.pcbi.1005220

PLOS Computational Biology Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist
December 8, 2016 Brian Drawert, Andreas Hellander, Ben Bales, Debjani Banerjee, Giovanni Bellesia, Bernie J. Daigle Jr., Geoffrey Douglas, Mengyuan Gu, Anand Gupta, Stefan Hellander, Chris Horuk, Dibyendu Nath, Aviral Takkar, Sheng Wu, Per Lötstedt, Chandra Krintz, Linda R. Petzold
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10.1371/journal.pcbi.1005096

PLOS Computational Biology AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework
October 5, 2016 Qi Zheng, Elizabeth A. Grice
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10.1371/journal.pcbi.1005112

PLOS Computational Biology Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline
September 23, 2016 Hao Chen, Mai Chan Lau, Michael Thomas Wong, Evan W. Newell, Michael Poidinger, Jinmiao Chen
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10.1371/journal.pcbi.1005115

PLOS Computational Biology M-Track: A New Software for Automated Detection of Grooming Trajectories in Mice
September 16, 2016 Sheldon L. Reeves, Kelsey E. Fleming, Lin Zhang, Annalisa Scimemi
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10.1371/journal.pcbi.1004751

PLOS Computational Biology metagene Profiles Analyses Reveal Regulatory Element’s Factor-Specific Recruitment Patterns
August 18, 2016 Charles Joly Beauparlant, Fabien C. Lamaze, Astrid Deschênes, Rawane Samb, Audrey Lemaçon, Pascal Belleau, Steve Bilodeau, Arnaud Droit
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10.1371/journal.pcbi.1004976

PLOS Computational Biology PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories
July 29, 2016 Victor Hanson-Smith, Alexander Johnson
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10.1371/journal.pcbi.1004978

PLOS Computational Biology Computationally Efficient Implementation of a Novel Algorithm for the General Unified Threshold Model of Survival (GUTS)
June 24, 2016 Carlo Albert, Roman Ashauer, Sören Vogel
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10.1371/journal.pcbi.1004809

PLOS Computational Biology QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks
June 23, 2016 Asa Thibodeau, Eladio J. Márquez, Oscar Luo, Yijun Ruan, Francesca Menghi, Dong-Guk Shin, Michael L. Stitzel, Paola Vera-Licona, Duygu Ucar
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10.1371/journal.pcbi.1004728

PLOS Computational Biology Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale
June 23, 2016 Daniel L. Parton, Patrick B. Grinaway, Sonya M. Hanson, Kyle A. Beauchamp, John D. Chodera
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10.1371/journal.pcbi.1004957

PLOS Computational Biology MEGAN Community Edition – Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data
June 21, 2016 Daniel H. Huson, Sina Beier, Isabell Flade, Anna Górska, Mohamed El-Hadidi, Suparna Mitra, Hans-Joachim Ruscheweyh, Rewati Tappu
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10.1371/journal.pcbi.1004753

PLOS Computational Biology GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research
June 16, 2016 Balázs Brankovics, Hao Zhang, Anne D. van Diepeningen, Theo A. J. van der Lee, Cees Waalwijk, G. Sybren de Hoog
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10.1371/journal.pcbi.1004980

PLOS Computational Biology FamPipe: An Automatic Analysis Pipeline for Analyzing Sequencing Data in Families for Disease Studies
June 6, 2016 Ren-Hua Chung, Wei-Yun Tsai, Chen-Yu Kang, Po-Ju Yao, Hui-Ju Tsai, Chia-Hsiang Chen
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10.1371/journal.pcbi.1004962

PLOS Computational Biology PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions
May 25, 2016 Jaroslav Bendl, Miloš Musil, Jan Štourač, Jaroslav Zendulka, Jiří Damborský, Jan Brezovský
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10.1371/journal.pcbi.1004925

PLOS Computational Biology PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies
May 25, 2016 Wenchao Zhang, Xinbin Dai, Qishan Wang, Shizhong Xu, Patrick X. Zhao
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10.1371/journal.pcbi.1004871

PLOS Computational Biology Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression
May 13, 2016 John Wiedenhoeft, Eric Brugel, Alexander Schliep
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10.1371/journal.pcbi.1004873

PLOS Computational Biology CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing
April 21, 2016 Eric Talevich, A. Hunter Shain, Thomas Botton, Boris C. Bastian
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10.1371/journal.pcbi.1004879

PLOS Computational Biology Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package
April 20, 2016 Nurcan Tuncbag, Sara J. C. Gosline, Amanda Kedaigle, Anthony R. Soltis, Anthony Gitter, Ernest Fraenkel
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10.1371/journal.pcbi.1004875

PLOS Computational Biology Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0
April 15, 2016 Brian R. Granger, Yi-Chien Chang, Yan Wang, Charles DeLisi, Zhenjun Hu, Daniel Segrè
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10.1371/journal.pcbi.1004794

PLOS Computational Biology SMOG 2: A Versatile Software Package for Generating Structure-Based Models
March 10, 2016 Jeffrey Noel, Mariana Levi, Mohit Raghunathan, Heiko Lammert, Ryan Hayes, Jose Onuchic, Paul Whitford
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Sydney Stringham

PLOS Computational Biology Wham: Identifying Structural Variants of Biological Consequence
December 1, 2015 Zev N. Kronenberg, Edward J. Osborne, Kelsey R. Cone, Brett J. Kennedy, Eric T. Domyan, Michael D. Shapiro, Nels C. Elde, Mark Yandell
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10.1371/journal.pcbi.1004503

PLOS Computational Biology VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires
November 25, 2015 Mikhail Shugay, Dmitriy V. Bagaev, Maria A. Turchaninova, Dmitriy A. Bolotin, Olga V. Britanova, Ekaterina V. Putintseva, Mikhail V. Pogorelyy, Vadim I. Nazarov, Ivan V. Zvyagin, Vitalina I. Kirgizova, Kirill I. Kirgizov, Elena V. Skorobogatova, Dmitriy M. Chudakov
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10.1371/journal.pcbi.1004575

PLOS Computational Biology SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis
November 24, 2015 Minzhe Guo, Hui Wang, S. Steven Potter, Jeffrey A. Whitsett, Yan Xu
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10.1371/journal.pcbi.1004415

PLOS Computational Biology ENCORE: Software for Quantitative Ensemble Comparison
October 27, 2015 Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, Kresten Lindorff-Larsen
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10.1371/journal.pcbi.1004401

PLOS Computational Biology TRANSIT – A Software Tool for Himar1 TnSeq Analysis
October 8, 2015 Michael A. DeJesus, Chaitra Ambadipudi, Richard Baker, Christopher Sassetti, Thomas R. Ioerger
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10.1371/journal.pcbi.1004447

PLOS Computational Biology ReproPhylo: An Environment for Reproducible Phylogenomics
September 3, 2015 Amir Szitenberg, Max John, Mark Blaxter, David Lunt
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10.1371/journal.pcbi.1004321

PLOS Computational Biology Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
August 27, 2015 Zachary A. King, Andreas Dräger, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, Bernhard O. Palsson
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10.1371/journal.pcbi.1004448

PLOS Computational Biology One Size Doesn’t Fit All – RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies
August 12, 2015 Shuai Yuan, Henry Johnston, Guosheng Zhang, Yun Li, Yijuan Hu, Zhaohui Qin
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10.1371/journal.pcbi.1004274

PLOS Computational Biology Genome Modeling System: A Knowledge Management Platform for Genomics
July 9, 2015 Malachi Griffith, Obi Griffith, Scott Smith, Avinash Ramu, Matthew Callaway, Anthony Brummett, Michael Kiwala, Adam Coffman, Allison Regier, Ben Oberkfell, Gabriel Sanderson, Thomas Mooney, Nathaniel Nutter, Edward Belter, Feiyu Du, Robert Long, Travis Abbott, Ian Ferguson, David Morton, Mark Burnett, James Weible, Joshua Peck, Adam Dukes, Joshua McMichael, Justin Lolofie, Brian Derickson, Jasreet Hundal, Zachary Skidmore, Benjamin Ainscough, Nathan Dees, William Schierding, Cyriac Kandoth, Kyung Kim, Charles Lu, Christopher Harris, Nicole Maher, Christopher Maher, Vincent Magrini, Benjamin Abbott, Ken Chen, Eric Clark, Indraniel Das, Xian Fan, Amy Hawkins, Todd Hepler, Todd Wylie, Shawn Leonard, William Schroeder, Xiaoqi Shi, Lynn Carmichael, Matthew Weil, Richard Wohlstadter, Gary Stiehr, Michael McLellan, Craig Pohl, Christopher Miller, Daniel Koboldt, Jason Walker, James Eldred, David Larson, David Dooling, Li Ding, Elaine Mardis, Richard Wilson
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10.1371/journal.pcbi.1004085

PLOS Computational Biology PathVisio 3: An Extendable Pathway Analysis Toolbox
February 23, 2015 Martina Kutmon, Martijn P. van Iersel, Anwesha Bohler, Thomas Kelder, Nuno Nunes, Alexander R. Pico, Chris T. Evelo
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10.1371/journal.pcbi.1003983

PLOS Computational Biology Integrative Multi-omics Module Network Inference with Lemon-Tree
February 13, 2015 Eric Bonnet, Laurence Calzone, Tom Michoel
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10.1371/journal.pcbi.1004041

PLOS Computational Biology ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
February 12, 2015 Xavier Didelot, Daniel J. Wilson
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10.1371/journal.pcbi.1004008

PLOS Computational Biology A RESTful API for Accessing Microbial Community Data for MG-RAST
January 8, 2015 Andreas Wilke, Jared Bischof, Travis Harrison, Thomas Brettin, Mark D'Souza, Wolfgang Gerlach, Hunter Matthews, Tobias Paczian, Jared Wilkening, Elizabeth Glass, Narayan Desai, Folker Meyer
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10.1371/journal.pcbi.1004022

PLOS Computational Biology Fast and Accurate Resonance Assignment of Small-to-Large Proteins by Combining Automated and Manual Approaches
January 8, 2015 Markus Niklasson, Alexandra Ahlner, Cecilia Andresen, Joseph Marsh, Patrik Lundström
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10.1371/journal.pcbi.1003880

PLOS Computational Biology FamSeq: A Variant Calling Program for Family-Based Sequencing Data Using Graphics Processing Units
October 30, 2014 Gang Peng, Yu Fan, Wenyi Wang
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10.1371/journal.pcbi.1003929

PLOS Computational Biology dcGOR: An R Package for Analysing Ontologies and Protein Domain Annotations
October 30, 2014 Hai Fang
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10.1371/journal.pcbi.1003842

PLOS Computational Biology IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform
September 25, 2014 N Hepler, Konrad Scheffler, Steven Weaver, Ben Murrell, Douglas Richman, Dennis Burton, Pascal Poignard, Davey Smith, Sergei Kosakovsky Pond
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10.1371/journal.pcbi.1003829

PLOS Computational Biology eMatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models
September 18, 2014 Michal Brylinski
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10.1371/journal.pcbi.1003841

PLOS Computational Biology NESmapper: Accurate Prediction of Leucine-Rich Nuclear Export Signals Using Activity-Based Profiles
September 18, 2014 Shunichi Kosugi, Hiroshi Yanagawa, Ryohei Terauchi, Satoshi Tabata
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10.1371/journal.pcbi.1003822

PLOS Computational Biology Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products
September 4, 2014 Marnix Medema, Yared Paalvast, Don Nguyen, Alexey Melnik, Pieter Dorrestein, Eriko Takano, Rainer Breitling
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10.1371/journal.pcbi.1003806

PLOS Computational Biology OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis
August 28, 2014 Greg Finak, Jacob Frelinger, Wenxin Jiang, Evan Newell, John Ramey, Mark Davis, Spyros Kalams, Stephen De Rosa, Raphael Gottardo
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10.1371/journal.pcbi.1003750

PLOS Computational Biology A Real-Time All-Atom Structural Search Engine for Proteins
July 31, 2014 Gabriel Gonzalez, Brett Hannigan, William F. DeGrado
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10.1371/journal.pcbi.1003702

PLOS Computational Biology CeleST: Computer Vision Software for Quantitative Analysis of C. elegans Swim Behavior Reveals Novel Features of Locomotion
July 17, 2014 Christophe Restif, Carolina Ibanez-Ventoso, Mehul Vora, Suzhen Guo, Dimitris Metaxas, Monica Driscoll
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10.1371/journal.pcbi.1003720

PLOS Computational Biology LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry
July 17, 2014 Jacob Durrant, Rommie Amaro
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PLOS

PLOS Computational Biology CGBayesNets: Conditional Gaussian Bayesian Network Learning and Inference with Mixed Discrete and Continuous Data
June 12, 2014 Michael J. McGeachie, Hsun-Hsien Chang, Scott T. Weiss
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10.1371/journal.pcbi.1003553

PLOS Computational Biology A Toolbox for Representational Similarity Analysis
April 17, 2014 Hamed Nili, Cai Wingfield, Li Su, Alexander Walther, William Marslen-Wilson, Nikolaus Kriegeskorte
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10.1371/journal.pcbi.1003537

PLOS Computational Biology BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
April 10, 2014 Remco Bouckaert, Josepeh Heled, Denise Kühnert, Tim Vaughan, Chieh-Hsi Wu, Dong Xie, Marc Suchard, Andrew Rambaut, Alexei Drummond
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10.1371/journal.pcbi.1003571

PLOS Computational Biology rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids
April 10, 2014 Sergio Ruiz-Carmona, Daniel Alvarez-Garcia, Nicolas Foloppe, A. Beatriz Garmendia-Doval, Szilveszter Juhos, Peter Schmidtke, Xavier Barril, Roderick Hubbard, S. David Morley
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10.1371/journal.pcbi.1003441

PLOS Computational Biology VBA: A Probabilistic Treatment of Nonlinear Models for Neurobiological and Behavioural Data
January 23, 2014 Jean Daunizeau, Vincent Adam, Lionel Rigoux
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10.1371/journal.pcbi.1003440

PLOS Computational Biology PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations
January 16, 2014 Jaroslav Bendl, Jan Stourac, Ondrej Salanda, Antonin Pavelka, Eric Wieben, Jaroslav Zendulka, Jan Brezovsky, Jiri Damborsky
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10.1371/journal.pcbi.1003270

PLOS Computational Biology CAPE: An R Package for Combined Analysis of Pleiotropy and Epistasis
October 24, 2013 Anna Tyler, Wei Lu, Justin Hendrick, Vivek Philip, Gregory Carter
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10.1371/journal.pcbi.1003234

PLOS Computational Biology ToPS: A Framework to Manipulate Probabilistic Models of Sequence Data
October 3, 2013 André Kashiwabara, Igor Bonadio, Vitor Onuchic, Felipe Amado, Rafael Mathias, Alan Durham
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PLOS

PLOS Computational Biology Using Biological Pathway Data with Paxtools
September 19, 2013 Emek Demir, Özgün Babur, Igor Rodchenkov, Bülent Arman Aksoy, Kenichiro Fukuda, Benjamin Gross, Onur Sümer, Gary Bader, Chris Sander
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10.1371/journal.pcbi.1003118

PLOS Computational Biology Software for Computing and Annotating Genomic Ranges
August 8, 2013 Michael Lawrence, Wolfgang Huber, Herve Pages, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin Morgan, Vince Carey
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10.1371/journal.pcbi.1003153

PLOS Computational Biology GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations
July 18, 2013 Umadevi Paila, Brad Chapman, Rory Kirchner, Aaron Quinlan
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10.1371/journal.pcbi.1002970

PLOS Computational Biology Chaste: An Open Source C++ Library for Computational Physiology and Biology
March 14, 2013 Gary Mirams, Christopher Arthurs, Miguel Bernabeu, Rafel Bordas, Jonathan Cooper, Alberto Corrias, Yohan Davit, Sara-Jane Dunn, Alexander Fletcher, Daniel Harvey, Megan Marsh, James Osborne, Pras Pathmanathan, Joe Pitt-Francis, James Southern, Nejib Zemzemi, David Gavaghan
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10.1371/journal.pcbi.1002916

PLOS Computational Biology Spartan: A Comprehensive Tool for Understanding Uncertainty in Simulations of Biological Systems
February 28, 2013 Kieran Alden, Mark Read, Jon Timmis, Paul Andrews, Henrique Veiga-Fernandes, Mark Coles
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PLOS

PLOS Computational Biology Standard Anatomical and Visual Space for the Mouse Retina: Computational Reconstruction and Transformation of Flattened Retinae with the Retistruct Package
February 28, 2013 David Sterratt, Daniel Lyngholm, David Willshaw, Ian Thompson
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10.1371/journal.pcbi.1002854

PLOS Computational Biology Getting More Out of Biomedical Documents with GATE’s Full Lifecycle Open Source Text Analytics
February 7, 2013 Hamish Cunningham, Valentin Tablan, Angus Roberts, Kalina Bontcheva
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10.1371/journal.pcbi.1002780

PLOS Computational Biology ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes
December 6, 2012 Kishore Mosaliganti, Ramil Noche, Fengzhu Xiong, Ian Swinburne, Sean Megason
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10.1371/journal.pcbi.1002708

PLOS Computational Biology CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
October 18, 2012 Eva Chovancova, Antonin Pavelka, Petr Benes, Ondrej Strnad, Jan Brezovsky, Barbora Kozlikova, Artur Gora, Vilem Sustr, Martin Klvana, Petr Medek, Lada Biedermannova, Jiri Sochor, Jiri Damborsky
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10.1371/journal.pcbi.1002628

PLOS Computational Biology Hybrid Models and Biological Model Reduction with PyDSTool
August 9, 2012 Robert Clewley
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10.1371/journal.pcbi.1002591

PLOS Computational Biology Automated Tracking of Whiskers in Videos of Head Fixed Rodents
July 5, 2012 Nathan Clack, Daniel O'Connor, Daniel Huber, Leopoldo Petreanu, Andrew Hires, Simon Peron, Karel Svoboda, Eugene Myers
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10.1371/journal.pcbi.1002567

PLOS Computational Biology ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin
June 28, 2012 John Capra, Alexander Williams, Katherine Pollard
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10.1371/journal.pcbi.1002529

PLOS Computational Biology Exploring Massive, Genome Scale Datasets with the GenometriCorr Package
May 31, 2012 Alexander Favorov, Loris Mularoni, Leslie Cope, Yulia Medvedeva, Andrey Mironov, Vsevolod Makeev, Sarah Wheelan
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10.1371/journal.pcbi.1002397

PLOS Computational Biology AutoClickChem: Click Chemistry in Silico
March 15, 2012 Jacob Durrant, J. McCammon
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10.1371/journal.pcbi.1002163

PLOS Computational Biology Podbat: A Novel Genomic Tool Reveals Swr1-Independent H2A.Z Incorporation at Gene Coding Sequences through Epigenetic Meta-Analysis
August 25, 2011 Laia Sadeghi, Carolina Bonilla, Annelie Strålfors, Karl Ekwall, J. Peter Svensson